In this thesis, the potential applications of reactive molecular dynamics in computational biology have been evaluated. Within the last three decades a considerable amount of simulations have been performed employing non-reactive molecular dynamics, which have had significant impacts on medicine and biomaterial sciences. However, we believe reactive molecular dynamics has the potentials to predict several vital events in human body that cannot be grasped either in experiment or other computational techniques. In this thesis, we briefly introduce the essence of reactive molecular techniques and show how this method can assist computational biologist to further analyze events that can ultimately lead to biochemical disorder by modeling two different systems (I) pH-drive helical coil transition to random coil and (II) graphene oxide interactions with polypeptide helices.
We have studied alpha helix to random coil transition using ReaxFF reactive molecular dynamics as a function of pH. In addition, we show proton transfer between the solution and the peptide can break the alpha helix hydrogen bonds and consequently, at extreme pHs significant amount of helix will unravel. We also compare the effects of temperature and alpha helix length in denaturation mechanism. The ReaxFF findings are in significant better agreement with ab initio calculations then previous non-reactive force field results – indicating the relevance of the reactive component on helical loss.
Furthermore, we report the first study on graphene oxide (GO) toxicity at the atomic scale. This study reveals the likely destructive mechanisms of GO during its interactions with living organisms. Reactive molecular dynamics study is utilized to illuminate the toxicity pathways and assess the available hypotheses about GO biocompatibility.